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It is a long time since I did this, but don't you need just one master mask - then that is converted using your rotation matrix to mask the related part of the structure ? Eleanor Dodson On 15 May 2012 15:56, Yu Feng <[log in to unmask]> wrote: > Dear De-Feng Li, > > Thank you for your reply. Actually, I already used the script. The script > and the log file are at the bottom of the email. > > Best wishes, > Yu > > > On Tue, May 15, 2012 at 3:18 AM, lidefeng <[log in to unmask]> wrote: > >> Dear Yu Feng, >> >> You could try it in script, but not in the CCP4i. The same >> problem could be found in DMMulti. >> >> Your sincerely >> De-Feng Li >> 2012-05-15 >> >> De-Feng Li, Ph.D, >> National Laboratory of Biomacromolecules >> Institute of Biophysics, Chinese Academy of Sciences >> 15 Datun Road, Chaoyang District >> Beijing 100101, PR China >> >> >> ======= 2012-05-15 18:44:48 You writed in your letter:======= >> >> >> >Dear CCP4ers, >> > >> >I have a problem when I use DM to do NCS averaging. If I input 9 NCS >> >averaging masks, DM works OK. However, if I input 10 NCS averaging masks, >> >DM can not open input map file. The masks should be OK because they are >> >generated by the same method. Do you have any idea how to solve the >> problem? >> > >> >Thank you in advance! >> >Yu >> > >> > >> >DM script is as below: >> >> >-------------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >/usr/share/CCP4-6.0.2/ccp4-6.2.0/bin/dm \ >> >hklin >> >> >/home/crystal/Documents/Ecoli/datasets/F111062011/130_10/reprocess/DM/xxxxx_refine33_phase.mtz >> >\ >> >ncsin1 E.msk \ >> >ncsin2 F1.msk \ >> >ncsin3 F2.msk \ >> >ncsin4 D4.msk \ >> >ncsin5 D5.msk \ >> >ncsin6 D3.msk \ >> >ncsin7 D2.msk \ >> >ncsin8 D1.msk \ >> >ncsin9 C5.msk \ >> >ncsin10 C6.msk \ >> >hklout xxxxx_dm.mtz <<EOF-dm >> >SOLC 0.62 >> >#RESOL 50 4.0 >> >#NCSMASK SIZE 100000000 >> >#NCSMASK UPDATE 3 >> >#GRID 144 144 144 >> >MODE SOLV hist AVER MULTI >> >combine weight 0.15 >> >combine pert >> >scheme res from 4.5 >> >NCYCLE 10 >> >ncsmask overlap >> >AVER DOMAIN 1 REFINE >> >ROTATE EULER 0.000 0.000 0.000 >> >TRANSLATION 0.000 0.000 0.000 >> > >> >AVER DOMAIN 1 REFINE >> >ROTA MATRIX -0.26665 0.52763 0.80654 0.60893 -0.55642 0.56533 0.74706 >> >0.64187 -0.17293 >> >TRAN -31.41600 172.23766 -96.59856 >> > >> >AVER DOMAIN 1 REFINE >> >ROTA MATRIX 0.82271 0.34200 -0.45406 -0.55866 0.63407 -0.53465 0.10506 >> >0.69353 0.71272 >> >TRAN -141.48692 39.40455 -17.81890 >> > >> >AVER DOMAIN 1 REFINE >> >ROTA MATRIX -0.35001 0.06658 0.93438 0.03939 -0.99554 0.08569 0.93592 >> >0.06679 0.34582 >> >TRAN -75.12174 220.50938 35.16329 >> > >> >AVER DOMAIN 2 REFIN >> >ROTATE EULER 0.000 0.000 0.000 >> >TRANSLATION 0.000 0.000 0.000 >> > >> >AVER DOMAIN 2 REFINE >> >ROTA MATRIX -0.42731 0.24363 0.87066 0.39149 -0.81818 0.42109 0.81494 >> >0.52080 0.25424 >> >TRAN -7.42336 185.84557 -68.83428 >> > >> >AVER DOMAIN 2 REFINE >> >ROTA MATRIX -0.42918 0.04126 0.90228 0.01801 -0.99837 0.05422 0.90304 >> >0.03952 0.42774 >> >TRAN -74.51554 219.69878 39.63858 >> > >> >AVER DOMAIN 2 REFINE >> >ROTA MATRIX 0.94716 0.32039 -0.01558 -0.30765 0.89358 -0.32691 -0.09082 >> >0.31442 0.94493 >> >TRAN -121.99072 28.41423 20.60830 >> > >> >AVER DOMAIN 3 REFINE >> >ROTATE EULER 0.000 0.000 0.000 >> >TRANSLATION 0.000 0.000 0.000 >> > >> >AVER DOMAIN 3 REFINE >> >ROTA MATRIX -0.42590 0.08845 0.90044 -0.00887 -0.99557 0.09361 0.90473 >> >0.03188 0.42480 >> >TRAN -77.38764 220.87816 40.52480 >> > >> >AVER DOMAIN 4 REFINE >> >ROTATE EULER 0.000 0.000 0.000 >> >TRANSLATION 0.000 0.000 0.000 >> > >> >AVER DOMAIN 4 REFINE >> >ROTA MATRIX -0.34404 0.07038 0.93631 -0.03070 -0.99750 0.06370 0.93845 >> >-0.00683 0.34534 >> >TRAN -79.74300 222.43433 43.52758 >> > >> >AVER DOMAIN 5 REFINE >> >ROTATE EULER 0.000 0.000 0.000 >> >TRANSLATION 0.000 0.000 0.000 >> > >> >AVER DOMAIN 5 REFINE >> >ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.99991 -0.01113 0.93309 >> >-0.01068 0.35948 >> >TRAN -70.14525 224.81303 43.77335 >> > >> >AVER DOMAIN 6 REFINE >> >ROTATE EULER 0.000 0.000 0.000 >> >TRANSLATION 0.000 0.000 0.000 >> > >> >AVER DOMAIN 6 REFINE >> >ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.99991 -0.01113 0.93309 >> >-0.01068 0.35948 >> >TRAN -70.14525 224.81303 43.77335 >> > >> >AVER DOMAIN 7 REFINE >> >ROTATE EULER 0.000 0.000 0.000 >> >TRANSLATION 0.000 0.000 0.000 >> > >> >AVER DOMAIN 7 REFINE >> >ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.99991 -0.01113 0.93309 >> >-0.01068 0.35948 >> >TRAN -70.14525 224.81303 43.77335 >> > >> >AVER DOMAIN 8 REFINE >> >ROTATE EULER 0.000 0.000 0.000 >> >TRANSLATION 0.000 0.000 0.000 >> > >> >AVER DOMAIN 8 REFINE >> >ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.99991 -0.01113 0.93309 >> >-0.01068 0.35948 >> >TRAN -70.14525 224.81303 43.77335 >> > >> >AVER DOMAIN 9 REFINE >> >ROTATE EULER 0.000 0.000 0.000 >> >TRANSLATION 0.000 0.000 0.000 >> > >> >AVER DOMAIN 9 REFINE >> >ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.99991 -0.01113 0.93309 >> >-0.01068 0.35948 >> >TRAN -70.14525 224.81303 43.77335 >> > >> >AVER DOMAIN 10 REFINE >> >ROTATE EULER 0.000 0.000 0.000 >> >TRANSLATION 0.000 0.000 0.000 >> > >> >AVER DOMAIN 10 REFINE >> >ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.99991 -0.01113 0.93309 >> >-0.01068 0.35948 >> >TRAN -70.14525 224.81303 43.77335 >> > >> >LABIN FP=FOBS SIGFP=SIGFOBS PHIO=PHIFMODEL FOMO=FOM >> >LABOUT PHIDM=PHIDM FOMDM=FOMDM >> >EOF-dm >> >> >------------------------------------------------------------------------------------------------------------------------------------------------------ >> > >> > >> > >> > >> >Part of the log file is as below: >> >> >------------------------------------------------------------------------------------------------------------------------------------------------------ >> > Grid dimensions 96 108 162 must contain the following prime >> > factors for agreement with symmetry restrictions- 2 2 2 >> > >> >>>>>>> CCP4 library signal library_file:Cannot open file (Error) >> > raised in ccp4_file_open2 <<<<<< >> >>>>>>> CCP4 library signal ccp4_map:Cannot open file (Error) >> > raised in ccp4_cmap_open <<<<<< >> >>>>>>> CCP4 library signal ccp4_map:Cannot open file (Error) >> > raised in MRDHDS <<<<<< >> > dm: Error in opening input map file. >> >Times: User: 0.1s System: 0.0s Elapsed: 0:00 >> ></pre> >> ></html> >> ><!--SUMMARY_END--></FONT></B> >> >> >--------------------------------------------------------------------------------------------------------------------------------------------------------- >> > >> >> ======================================================== >> >> >> >> >> >